rs200823300
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_022489.4(INF2):c.3637C>T(p.Arg1213Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000413 in 1,596,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1213Q) has been classified as Likely benign.
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.3637C>T | p.Arg1213Trp | missense_variant | 21/23 | ENST00000392634.9 | |
INF2 | NM_001031714.4 | c.3637C>T | p.Arg1213Trp | missense_variant | 21/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.3637C>T | p.Arg1213Trp | missense_variant | 21/23 | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000373 AC: 8AN: 214612Hom.: 0 AF XY: 0.0000336 AC XY: 4AN XY: 119056
GnomAD4 exome AF: 0.0000436 AC: 63AN: 1444644Hom.: 0 Cov.: 36 AF XY: 0.0000362 AC XY: 26AN XY: 718276
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152282Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74464
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at